1
|
Nazarova A, Shiabiev I, Shibaeva K, Mostovaya O, Mukhametzyanov T, Khannanov A, Evtugyn V, Zelenikhin P, Shi X, Shen M, Padnya P, Stoikov I. Thiacalixarene Carboxylic Acid Derivatives as Inhibitors of Lysozyme Fibrillation. Int J Mol Sci 2024; 25:4721. [PMID: 38731940 PMCID: PMC11083589 DOI: 10.3390/ijms25094721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Amyloid fibroproliferation leads to organ damage and is associated with a number of neurodegenerative diseases affecting populations worldwide. There are several ways to protect against fibril formation, including inhibition. A variety of organic compounds based on molecular recognition of amino acids within the protein have been proposed for the design of such inhibitors. However, the role of macrocyclic compounds, i.e., thiacalix[4]arenes, in inhibiting fibrillation is still almost unknown. In the present work, the use of water-soluble thiacalix[4]arene derivatives for the inhibition of hen egg-white lysozyme (HEWL) amyloid fibrillation is proposed for the first time. The binding of HEWL by the synthesized thiacalix[4]arenes (logKa = 5.05-5.13, 1:1 stoichiometry) leads to the formation of stable supramolecular systems capable of stabilizing the protein structure and protecting against fibrillation by 29-45%. The macrocycle conformation has little effect on protein binding strength, and the native HEWL secondary structure does not change via interaction. The synthesized compounds are non-toxic to the A549 cell line in the range of 0.5-250 µg/mL. The results obtained may be useful for further investigation of the anti-amyloidogenic role of thiacalix[4]arenes, and also open up future prospects for the creation of new ways to prevent neurodegenerative diseases.
Collapse
Affiliation(s)
- Anastasia Nazarova
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Igor Shiabiev
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Ksenia Shibaeva
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Olga Mostovaya
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Timur Mukhametzyanov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Arthur Khannanov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Vladimir Evtugyn
- Interdisciplinary Center of Analytical Microscopy, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Pavel Zelenikhin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
- CQM—Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105 Funchal, Portugal
| | - Mingwu Shen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Pavel Padnya
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| | - Ivan Stoikov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 18 Kremlyovskaya Str., 420008 Kazan, Russia
| |
Collapse
|
2
|
Porfetye AT, Stege P, Rebollido-Rios R, Hoffmann D, Schrader T, Vetter IR. How Do Molecular Tweezers Bind to Proteins? Lessons from X-ray Crystallography. Molecules 2024; 29:1764. [PMID: 38675584 PMCID: PMC11051928 DOI: 10.3390/molecules29081764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
To understand the biological relevance and mode of action of artificial protein ligands, crystal structures with their protein targets are essential. Here, we describe and investigate all known crystal structures that contain a so-called "molecular tweezer" or one of its derivatives with an attached natural ligand on the respective target protein. The aromatic ring system of these compounds is able to include lysine and arginine side chains, supported by one or two phosphate groups that are attached to the half-moon-shaped molecule. Due to their marked preference for basic amino acids and the fully reversible binding mode, molecular tweezers are able to counteract pathologic protein aggregation and are currently being developed as disease-modifying therapies against neurodegenerative diseases such as Alzheimer's and Parkinson's disease. We analyzed the corresponding crystal structures with 14-3-3 proteins in complex with mono- and diphosphate tweezers. Furthermore, we solved crystal structures of two different tweezer variants in complex with the enzyme Δ1-Pyrroline-5-carboxyl-dehydrogenase (P5CDH) and found that the tweezers are bound to a lysine and methionine side chain, respectively. The different binding modes and their implications for affinity and specificity are discussed, as well as the general problems in crystallizing protein complexes with artificial ligands.
Collapse
Affiliation(s)
- Arthur T. Porfetye
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Patricia Stege
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Rocio Rebollido-Rios
- Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Daniel Hoffmann
- Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Ingrid R. Vetter
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| |
Collapse
|
3
|
Bartocci A, Dumont E. Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations. J Chem Phys 2024; 160:105101. [PMID: 38465686 DOI: 10.1063/5.0198522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.
Collapse
Affiliation(s)
- Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| |
Collapse
|
4
|
Lazar AN, Perret F, Perez-Lloret M, Michaud M, Coleman AW. Promises of anionic calix[n]arenes in life science: State of the art in 2023. Eur J Med Chem 2024; 264:115994. [PMID: 38070431 DOI: 10.1016/j.ejmech.2023.115994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
Because they hold together molecules by means of non-covalent interactions - relatively weak and thus, potentially reversible - the anionic calixarenes have become an interesting tool for efficiently binding a large range of ligands - from gases to large organic molecules. Being highly water soluble and conveniently biocompatible, they showed growing interest for many interdisciplinary fields, particularly in biology and medicine. Thanks to their intrinsic conical shape, they provide suitable platforms, from vesicles to bilayers. This is a valuable characteristic, as so they mimic the biologically functional architectures. The anionic calixarenes propose efficient alternatives for overcoming the limitations linked to drug delivery and bioavailability, as well as drug resistance along with limiting the undesirable side effects. Moreover, the dynamic non-covalent binding with the drugs enables predictable and on demand drug release, controlled by the stimuli present in the targeted environment. This particular feature instigated the use of these versatile, stimuli-responsive compounds for sensing biomarkers of diverse pathologies. The present review describes the recent achievements of the anionic calixarenes in the field of life science, from drug carriers to biomedical engineering, with a particular outlook on their applications for the diagnosis and treatment of different pathologies.
Collapse
Affiliation(s)
- Adina-N Lazar
- Univ Lyon, INSA-Lyon, CNRS UMR5259, LaMCoS, F-69621, France.
| | - Florent Perret
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246, Univ. Lyon - CNRS - Univ. Claude Bernard Lyon 1 - CPE Lyon, 43 Boulevard du 11 Novembre 1918, Villeurbanne, 69622, Cedex, France.
| | - Marta Perez-Lloret
- School of Biological and Chemical Sciences, University of Galway, Ireland Galway, Ireland
| | - Mickael Michaud
- CIRI, Univ. Lyon1, Inserm, U1111, CNRS, UMR5308, ENS, Lyon, France
| | | |
Collapse
|
5
|
Selinger AJ, Hof F. Adaptive Supramolecular Networks: Emergent Sensing from Complex Systems. Angew Chem Int Ed Engl 2023; 62:e202312407. [PMID: 37699200 DOI: 10.1002/anie.202312407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
Molecular differentiation by supramolecular sensors is typically achieved through sensor arrays, relying on the pattern recognition responses of large panels of isolated sensing elements. Here we report a new one-pot systems chemistry approach to differential sensing in biological solutions. We constructed an adaptive network of three cross-assembling sensor elements with diverse analyte-binding and photophysical properties. This robust sensing approach exploits complex interconnected sensor-sensor and sensor-analyte equilibria, producing emergent supramolecular and photophysical responses unique to each analyte. We characterize the basic mechanisms by which an adaptive network responds to analytes. The inherently data-rich responses of an adaptive network discriminate among very closely related proteins and protein mixtures without relying on designed protein recognition elements. We show that a single adaptive sensing solution provides better analyte discrimination using fewer response observations than a sensor array built from the same components. We also show the network's ability to adapt and respond to changing biological solutions over time.
Collapse
Affiliation(s)
- Allison J Selinger
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
| |
Collapse
|
6
|
Seiler T, Lennartz A, Klein K, Hommel K, Figueroa Bietti A, Hadrovic I, Kollenda S, Sager J, Beuck C, Chlosta E, Bayer P, Juul-Madsen K, Vorup-Jensen T, Schrader T, Epple M, Knauer SK, Hartmann L. Potentiating Tweezer Affinity to a Protein Interface with Sequence-Defined Macromolecules on Nanoparticles. Biomacromolecules 2023; 24:3666-3679. [PMID: 37507377 DOI: 10.1021/acs.biomac.3c00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Survivin, a well-known member of the inhibitor of apoptosis protein family, is upregulated in many cancer cells, which is associated with resistance to chemotherapy. To circumvent this, inhibitors are currently being developed to interfere with the nuclear export of survivin by targeting its protein-protein interaction (PPI) with the export receptor CRM1. Here, we combine for the first time a supramolecular tweezer motif, sequence-defined macromolecular scaffolds, and ultrasmall Au nanoparticles (us-AuNPs) to tailor a high avidity inhibitor targeting the survivin-CRM1 interaction. A series of biophysical and biochemical experiments, including surface plasmon resonance measurements and their multivalent evaluation by EVILFIT, reveal that for divalent macromolecular constructs with increasing linker distance, the longest linkers show superior affinity, slower dissociation, as well as more efficient PPI inhibition. As a drawback, these macromolecular tweezer conjugates do not enter cells, a critical feature for potential applications. The problem is solved by immobilizing the tweezer conjugates onto us-AuNPs, which enables efficient transport into HeLa cells. On the nanoparticles, the tweezer valency rises from 2 to 16 and produces a 100-fold avidity increase. The hierarchical combination of different scaffolds and controlled multivalent presentation of supramolecular binders was the key to the development of highly efficient survivin-CRM1 competitors. This concept may also be useful for other PPIs.
Collapse
Affiliation(s)
- Theresa Seiler
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstraße 1, Duesseldorf 40225, Germany
| | - Annika Lennartz
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Kai Klein
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Katrin Hommel
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Antonio Figueroa Bietti
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Inesa Hadrovic
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Sebastian Kollenda
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Jonas Sager
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Emilia Chlosta
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Kristian Juul-Madsen
- Department of Biomedicine, Aarhus University, Skou Building (1115), Høegh-Guldbergs Gade 10, DK-8000 Aarhus C, Denmark
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Vorup-Jensen
- Department of Biomedicine, Aarhus University, Skou Building (1115), Høegh-Guldbergs Gade 10, DK-8000 Aarhus C, Denmark
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Shirley K Knauer
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Laura Hartmann
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstraße 1, Duesseldorf 40225, Germany
| |
Collapse
|
7
|
Martinez Morales M, van der Walle CF, Derrick JP. Modulation of the Fibrillation Kinetics and Morphology of a Therapeutic Peptide by Cucurbit[7]uril. Mol Pharm 2023. [PMID: 37327060 DOI: 10.1021/acs.molpharmaceut.3c00185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fibrillation is a challenge commonly encountered in the formulation and development of therapeutic peptides. Cucurbit[7]urils (CB[7]), a group of water soluble macrocycles, have been reported to suppress fibrillation in insulin and human calcitonin through association with Phe and Tyr residues which drive fibril formation. Here, we report the effect of CB[7] on the fibrillation behavior of the HIV fusion inhibitor enfuvirtide (ENF) that contains N-terminal Tyr and C-terminal Phe residues. Thioflavin T fluorescence, CD spectroscopy, and transmission electron microscopy were used to monitor fibrillation behavior. Fibrillation onset showed a strong pH dependency, with pH 6.5 identified as the condition most suitable to monitor the effects of CB[7]. Binding of CB[7] to wild-type ENF was measured by isothermal titration calorimetry and was consistent with a single site (Ka = 2.4 × 105 M-1). A weaker interaction (Ka = 2.8 × 103 M-1) was observed for an ENF mutant with the C-terminal Phe substituted for Ala (ENFm), suggesting that Phe was the specific site for CB[7] recognition. The onset of ENF fibrillation onset was delayed, rather than fully suppressed, in the presence of CB[7]. The ENFm mutant showed a greater delay in fibrillation onset but with no observable effect on fibrillation kinetics in the presence of CB[7]. Interestingly, ENF/CB[7] and ENFm fibrils exhibited comparable morphologies, differing from those observed for ENF alone. The results indicate that CB[7] is capable of modulating fibrillation onset and the resulting ENF fibrils by specifically binding to the C-terminal Phe residue. The work reinforces the potential of CB[7] as an inhibitor of fibrillation and highlights its role in determining fibril morphologies.
Collapse
Affiliation(s)
- Marcello Martinez Morales
- Dosage Form Design & Development, AstraZeneca, Aaron Klug Building, Granta Park, Cambridge CB21 6GH, U.K
- School of Biological Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PL, U.K
| | | | - Jeremy P Derrick
- School of Biological Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PL, U.K
| |
Collapse
|
8
|
Saibu OA, Hammed SO, Oladipo OO, Odunitan TT, Ajayi TM, Adejuyigbe AJ, Apanisile BT, Oyeneyin OE, Oluwafemi AT, Ayoola T, Olaoba OT, Alausa AO, Omoboyowa DA. Protein-protein interaction and interference of carcinogenesis by supramolecular modifications. Bioorg Med Chem 2023; 81:117211. [PMID: 36809721 DOI: 10.1016/j.bmc.2023.117211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.
Collapse
Affiliation(s)
- Oluwatosin A Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, NorthRhine-Westphalia, Germany
| | - Sodiq O Hammed
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Tope T Odunitan
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Aderonke J Adejuyigbe
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwatoba E Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Adenrele T Oluwafemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tolulope Ayoola
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olamide T Olaoba
- Department of Molecular Pathogenesis and Therapeutics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Abdullahi O Alausa
- Department of Molecular Biology and Biotechnology, ITMO University, St Petersburg, Russia
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| |
Collapse
|
9
|
Aggarwal S, Ikram S. A comprehensive review on bio-mimicked multimolecular frameworks and supramolecules as scaffolds for enzyme immobilization. Biotechnol Bioeng 2023; 120:352-398. [PMID: 36349456 DOI: 10.1002/bit.28282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/30/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Immobilization depicts a propitious route to optimize the catalytic performances, efficient recovery, minimizing autocatalysis, and also augment the stabilities of enzymes, particularly in unnatural environments. In this opinion, supramolecules and multimolecular frameworks have captivated immense attention to achieve profound controllable interactions between enzyme molecules and well-defined natural or synthetic architectures to yield protein bioconjugates with high accessibility for substrate binding and enhanced enantioselectivities. This scholastic review emphasizes the possibilities of associating multimolecular complexes with biological entities via several types of interactions, namely covalent interactions, host-guest complexation, π - π ${\rm{\pi }}-{\rm{\pi }}$ interactions, intra/inter hydrogen bondings, electrostatic interactions, and so forth offers remarkable applications for the modulations of enzymes. The potential synergies between artificial supramolecular structures and biological systems are the primary concern of this pedagogical review. The majority of the research primarily focused on the dynamic biomolecule-responsive supramolecular assemblages and multimolecular architectures as ideal platforms for the recognition and modulation of proteins and cells. Embracing sustainable green demeanors of enzyme immobilizations in a quest to reinforce site-selectivity, catalytic efficiency, and structural integrality of enzymes are the contemporary requirements of the biotechnological sectors that instigate the development of novel biocatalytic systems.
Collapse
Affiliation(s)
- Shalu Aggarwal
- Bio/Polymers Research Laboratory, Department of Chemistry, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Saiqa Ikram
- Bio/Polymers Research Laboratory, Department of Chemistry, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
10
|
Bartocci A, Pereira G, Cecchini M, Dumont E. Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment. J Chem Inf Model 2022; 62:6739-6748. [PMID: 36054284 DOI: 10.1021/acs.jcim.2c00483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Calix[n]arenes' selective recognition of protein surfaces covers a broad range of timely applications, from controlling protein assembly and crystallization to trapping partially disordered proteins. Here, the interaction of para-sulfonated calix-[4]-arenes with cytochrome c is investigated through all-atom, explicit water molecular dynamics simulations which allow characterization of two binding sites in quantitative agreement with experimental evidence. Free energy calculations based on the MM-PBSA and the attach-pull-release (APR) methods highlight key residues implicated in the recognition process and provide binding free energy results in quantitative agreement with isothermal titration calorimetry. Our study emphasizes the role of MD simulations to capture and describe the "walk" of sulfonated calix-[4]-arenes on the cytochrome c surface, with the arginine R13 as a pivotal interacting residue. Our MD investigation allows, through the quasi-harmonic multibasin (QHMB) method, probing an allosteric reinforcement of several per-residue interactions upon calixarene binding, which suggests a more complex mode of action of these supramolecular auxiliaries.
Collapse
Affiliation(s)
- Alessio Bartocci
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, F-69342 Lyon, France.,Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France
| | - Gilberto Pereira
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France.,Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France
| | - Elise Dumont
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, F-69342 Lyon, France.,Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| |
Collapse
|
11
|
Volpi S, Doolan A, Baldini L, Casnati A, Crowley PB, Sansone F. Complex Formation between Cytochrome c and a Tetra-alanino-calix[4]arene. Int J Mol Sci 2022; 23:ijms232315391. [PMID: 36499717 PMCID: PMC9737847 DOI: 10.3390/ijms232315391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Owing to their remarkable features, calix[n]arenes are being exploited to study different aspects of molecular recognition, including protein complexation. Different complexation modes have been described, depending on the moieties that complement the aromatic cavity, allowing for function regulation and/or controlled assembly of the protein target. Here, a rigid cone calix[4]arene, bearing four anionic alanine units at the upper rim, was tested as a ligand for cytochrome c. Cocrystallization attempts were unfruitful, preventing a solid-state study of the system. Next, the complex was studied using NMR spectroscopy, which revealed the presence of two binding sites at lysine residues with dissociation constants (Kd) in the millimolar range.
Collapse
Affiliation(s)
- Stefano Volpi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
| | - Aishling Doolan
- School of Biological and Chemical Sciences, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Laura Baldini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
- Correspondence:
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
| | - Peter B. Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Francesco Sansone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze, 17/A, 43124 Parma, Italy
| |
Collapse
|
12
|
Höing A, Kirupakaran A, Beuck C, Pörschke M, Niemeyer FC, Seiler T, Hartmann L, Bayer P, Schrader T, Knauer SK. Recognition of a Flexible Protein Loop in Taspase 1 by Multivalent Supramolecular Tweezers. Biomacromolecules 2022; 23:4504-4518. [PMID: 36200481 DOI: 10.1021/acs.biomac.2c00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many natural proteins contain flexible loops utilizing well-defined complementary surface regions of their interacting partners and usually undergo major structural rearrangements to allow perfect binding. The molecular recognition of such flexible structures is still highly challenging due to the inherent conformational dynamics. Notably, protein-protein interactions are on the other hand characterized by a multivalent display of complementary binding partners to enhance molecular affinity and specificity. Imitating this natural concept, we here report the rational design of advanced multivalent supramolecular tweezers that allow addressing two lysine and arginine clusters on a flexible protein surface loop. The protease Taspase 1, which is involved in cancer development, carries a basic bipartite nuclear localization signal (NLS) and thus interacts with Importin α, a prerequisite for proteolytic activation. Newly established synthesis routes enabled us to covalently fuse several tweezer molecules into multivalent NLS ligands. The resulting bi- up to pentavalent constructs were then systematically compared in comprehensive biochemical assays. In this series, the stepwise increase in valency was robustly reflected by the ligands' gradually enhanced potency to disrupt the interaction of Taspase 1 with Importin α, correlated with both higher binding affinity and inhibition of proteolytic activity.
Collapse
Affiliation(s)
- Alexander Höing
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Abbna Kirupakaran
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Marius Pörschke
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Felix C Niemeyer
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Theresa Seiler
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Laura Hartmann
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| |
Collapse
|
13
|
Exploring Inclusion Complexes of Amino Acids with -Sulfonatothiacalix[4]arene by Experimental and Computational Approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
14
|
Abstract
ConspectusThis Account summarizes the progress in protein-calixarene complexation, tracing the developments from binary recognition to the glue activity of calixarenes and beyond to macrocycle-mediated frameworks. During the past 10 years, we have been tackling the question of protein-calixarene complexation in several ways, mainly by cocrystallization and X-ray structure determination as well as by solution state methods, NMR spectroscopy, isothermal titration calorimetry (ITC), and light scattering. Much of this work benefitted from collaboration, highlighted here. Our first breakthrough was the cocrystallization of cationic cytochrome c with sulfonato-calix[4]arene leading to a crystal structure defining three binding sites. Together with NMR studies, a dynamic complexation was deduced in which the calixarene explores the protein surface. Other cationic proteins were similarly amenable to cocrystallization with sulfonato-calix[4]arene, confirming calixarene-arginine/lysine encapsulation and consequent protein assembly. Calixarenes bearing anionic substituents such as sulfonate or phosphonate, but not carboxylate, have proven useful.Studies with larger calix[n]arenes (n = 6, 8) demonstrated the bigger better binder phenomenon with increased affinities and more interesting assemblies, including solution-state oligomerization and porous frameworks. While the calix[4]arene cavity accommodates a single cationic side chain, the larger macrocycles adopt different conformations, molding to the protein surface and accommodating several residues (hydrophobic, polar, and/or charged) in small cavities. In addition to accommodating protein features, the calixarene can bind exogenous components such as polyethylene glycol (PEG), metal ions, buffer, and additives. Ternary cocrystallization of cytochrome c, sulfonato-calix[8]arene, and spermine resulted in altered framework fabrication due to calixarene encapsulation of the tetraamine. Besides host-guest chemistry with exogenous components, the calixarene can also self-assemble, with numerous instances of macrocycle dimers.Calixarene complexation enables protein encapsulation, not merely side chain encapsulation. Cocrystal structures of sulfonato-calix[8]arene with cytochrome c or Ralstonia solanacearum lectin (RSL) provide evidence of encapsulation, with multiple calixarenes masking the same protein. NMR studies of cytochrome c and sulfonato-calix[8]arene are also consistent with multisite binding. In the case of RSL, a C3 symmetric trimer, up to six calixarenes bind the protein yielding a cubic framework mediated by calixarene dimers. Biomolecular calixarene complexation has evolved from molecular recognition to framework construction. This latter development contributes to the challenge in design and preparation of porous molecular materials. Cytochrome c and sulfonato-calix[8]arene form frameworks with >60% solvent in which the degree of porosity depends on the protein:calixarene ratio and the crystallization conditions. Recent developments with RSL led to three frameworks with varying porosity depending on the crystallization conditions, particularly the pH. NMR studies indicate a pH-triggered assembly in which two acidic residues appear to play key roles. The field of supramolecular protein chemistry is growing, and this Account aims to encourage new developments at the interface between biomolecular and synthetic/supramolecular chemistry.
Collapse
Affiliation(s)
- Peter B Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
| |
Collapse
|
15
|
Dai XY, Zhang B, Yu Q, Liu Y. In Situ Coassembly Induced Mitochondrial Aggregation Activated Drug-Resistant Tumor Treatment. J Med Chem 2022; 65:7363-7370. [PMID: 35579431 DOI: 10.1021/acs.jmedchem.2c00372] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Macrocyclic supramolecular coassembly is the current research hotspot for tumor treatment. Herein, we report a multivalent supramolecular coassembly strategy, which not only acquires long-time phosphorescent labeling of mitochondrial aggregation but also strongly enhances chemotherapeutic efficiency against drug-resistant tumors. The mitochondrial aggregation depends on cucurbit[8]uril-mediated cross-linkage of the hyaluronic acid polymer grafted by 4-bromophenylpyridium and mitochondrion-targeting peptide (HABMitP) residing on the mitochondria, taking advantage of the 2:1 homoternary host-guest complexation between cucurbit[8]uril and 4-bromophenylpyridium with an extraordinary binding constant (6.24 × 1012 M-2). In cisplatin-resistant MCF-7 tumor cells, the assembly induced mitochondrial aggregation substantially enhances the antitumor efficiency of cisplatin, with the ratio of apoptotic cells increasing from 43% to 96% compared to treatment with cisplatin alone, and thoroughly inhibits tumor growth in vivo. This study provides a novel way for biological phosphorescent imaging and treatment of drug-resistant cancers.
Collapse
Affiliation(s)
- Xian-Yin Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Bing Zhang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| |
Collapse
|
16
|
Veettil SP, Gopinath A, Madhan B, Shanmugam G. A cyclodextrin-based macrocyclic oligosaccharide cavitand with a dual functionality limits the collagen fibrillogenesis: A possible carbohydrate-based therapeutic molecule for fibrotic diseases. Int J Biol Macromol 2022; 207:222-231. [PMID: 35259432 DOI: 10.1016/j.ijbiomac.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/16/2022] [Accepted: 03/02/2022] [Indexed: 11/05/2022]
Abstract
β-Cyclodextrin (β-CD), a macrocyclic oligosaccharide cavitand, is a well-known candidate for drug delivery and formulation. In this study, we extended the application of β-CD using a β-cyclodextrin sulfate (β-CDS) as a possible therapeutic for fibrotic diseases caused by excess deposition of collagen fibrils. We have strategically chosen β-CDS, which mimics the natural existence of dermatan sulfate in the extracellular matrix, for limiting collagen fibrillation. The hydrophobic nature of the inner core β-CDS is expected to form an inclusion complex with hydrophobic side chain amino acids with the simultaneous action of forming an ionic bond through a negative charge on sulfate group with positively charged amino acids side chain in collagen. Various results suggested that such dual action not only limited the collagen fibrillation but also reduced the fibril size formed in the presence of β-CDS. The contemporary results thus indicate that β-CDS can be explored as a therapeutic molecule in fibrotic diseases.
Collapse
Affiliation(s)
- Sruthi Puthan Veettil
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India
| | - Arun Gopinath
- CARE Division, CSIR-CLRI, Adyar, Chennai 600020, India
| | | | - Ganesh Shanmugam
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India.
| |
Collapse
|
17
|
Zhou X, Shi M, Wang X, Xu D. Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ Protein via Well-Tempered Metadynamics. Front Chem 2022; 10:921695. [PMID: 35646830 PMCID: PMC9133541 DOI: 10.3389/fchem.2022.921695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Using supramolecules for protein function regulation is an effective strategy in chemical biology and drug discovery. However, due to the presence of multiple binding sites on protein surfaces, protein function regulation via selective binding of supramolecules is challenging. Recently, the functions of 14-3-3 proteins, which play an important role in regulating intracellular signaling pathways via protein–protein interactions, have been modulated using a supramolecular tweezer, CLR01. However, the binding mechanisms of the tweezer molecule to 14-3-3 proteins are still unclear, which has hindered the development of novel supramolecules targeting the 14-3-3 proteins. Herein, the binding mechanisms of the tweezer to the lysine residues on 14-3-3σ (an isoform in 14-3-3 protein family) were explored by well-tempered metadynamics. The results indicated that the inclusion complex formed between the protein and supramolecule is affected by both kinetic and thermodynamic factors. In particular, simulations confirmed that K214 could form a strong binding complex with the tweezer; the binding free energy was calculated to be −10.5 kcal·mol−1 with an association barrier height of 3.7 kcal·mol−1. In addition, several other lysine residues on 14-3-3σ were identified as being well-recognized by the tweezer, which agrees with experimental results, although only K214/tweezer was co-crystallized. Additionally, the binding mechanisms of the tweezer to all lysine residues were analyzed by exploring the representative conformations during the formation of the inclusion complex. This could be helpful for the development of new inhibitors based on tweezers with more functions against 14-3-3 proteins via modifications of CLR01. We also believe that the proposed computational strategies can be extended to understand the binding mechanism of multi-binding sites proteins with supramolecules and will, thus, be useful toward drug design.
Collapse
Affiliation(s)
- Xin Zhou
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
| |
Collapse
|
18
|
Flood R, Ramberg KO, Mengel DB, Guagnini F, Crowley PB. Protein Frameworks with Thiacalixarene and Zinc. CRYSTAL GROWTH & DESIGN 2022; 22:3271-3276. [PMID: 35529063 PMCID: PMC9073927 DOI: 10.1021/acs.cgd.2c00108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/10/2022] [Indexed: 05/15/2023]
Abstract
Controlled protein assembly provides a means to generate biomaterials. Synthetic macrocycles such as the water-soluble sulfonato-calix[n]arenes are useful mediators of protein assembly. Sulfonato-thiacalix[4]arene (tsclx 4 ), with its metal-binding capacity, affords the potential for simultaneous macrocycle- and metal-mediated protein assembly. Here, we describe the tsclx 4 -/Zn-directed assembly of two proteins: cationic α-helical cytochrome c (cyt c) and neutral β-propeller Ralstonia solanacearum lectin (RSL). Two co-crystal forms were obtained with cyt c, each involving multinuclear zinc sites supported by the cone conformation of tsclx 4 . The tsclx 4 /Zn cluster acted as an assembly node via both lysine encapsulation and metal-mediated protein-protein contacts. In the case of RSL, tsclx 4 adopted the 1,2-alternate conformation and supported a dinuclear zinc site with concomitant encapsulation and metal-binding of two histidine side chains. These results, together with the knowledge of thiacalixarene/metal nanoclusters, suggest promising applications for thiacalixarenes in biomaterials and MOF fabrication.
Collapse
|
19
|
Zhang ZY, Li C. Biphen[ n]arenes: Modular Synthesis, Customizable Cavity Sizes, and Diverse Skeletons. Acc Chem Res 2022; 55:916-929. [PMID: 35239333 DOI: 10.1021/acs.accounts.2c00043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Macrocyclic compounds are fundamental tools in supramolecular chemistry and have been widely used in molecular recognition, biomedicine, and materials science. The construction of new macrocycles with distinctive structures and properties would unleash new opportunities for supramolecular chemistry. Traditionally popular macrocycles, e.g., cyclodextrins, calixarenes, cucurbiturils, and pillararenes, possess specific cavities that are usually less than 10 Å in diameter; they are normally suitable for accommodating small- or medium-sized guests but cannot engulf giant molecules or structures. Furthermore, the skeletons of traditional macrocycles are impoverished and incapable of being changed; functional substituents can be introduced only on their portals.Thus, it is very challenging to construct macrocycles with customizable cavity sizes and/or diverse backbones. We have developed a versatile and modular strategy for synthesizing macrocycles, namely, biphen[n]arenes (n = 3-8), based on the structure- or function-oriented replacement of reaction modules, functional modules, and linking modules. First, two reaction modules and one functional module are connected by Suzuki-Miyaura coupling to obtain a monomer having two reaction sites. Then Friedel-Crafts alkylation between the monomer and an aldehyde (linking module) serves to afford diversely functionalized macrocycles. Moreover, large macrocycles can be achieved by using long and rigid oligo(para-phenylene) monomers. Because of the modular synthesis and plentiful molecular supplies, the biphen[n]arenes showed interesting recognition properties for both small molecules and large polypeptides. Customizable functional backbones and binding sites endowed this new family of macrocycles with peculiar self-assembly properties and potential applications in gas chromatography, pollutant capture, and physisorptive separation. Biphen[n]arenes would be a promising family of workhorses in supramolecular chemistry.In this Account, we summarize our recent work on the chemistry of biphen[n]arenes. We introduce their design and modular synthesis, including systematic exploration for reaction modules, customizable cavity sizes, skeleton functionalization, pre- and postmodification, and molecular cages. Thereafter, we discuss their host-guest properties, involving the binding for small guests by cationic/anionic/neutral biphen[n]arenes, as well as the complexation of polypeptides by large quaterphen[n]arenes. In addition, we outline the self-assembly and potential applications of this new family of macrocycles. Finally, we forecast their further development. The chemistry of biphen[n]arenes is still in its infancy. Continued exploration will not only further expand the supramolecular toolbox but also open new avenues for the use of biphen[n]arenes in the fields of biology, pharmaceutical science, and materials science.
Collapse
Affiliation(s)
- Zhi-Yuan Zhang
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, College of Chemistry, Tianjin Normal University, Tianjin 300387, P. R. China
| | - Chunju Li
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, College of Chemistry, Tianjin Normal University, Tianjin 300387, P. R. China
| |
Collapse
|
20
|
Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
Collapse
Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| |
Collapse
|
21
|
Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
Collapse
Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| |
Collapse
|
22
|
Bodoor K, El-Barghouthi MI, Assaf KI, Al Hourani BJ, Rawashdeh AMM, Abuhasan OM, Alhamad DF, Abdel-Halim HM. A molecular dynamics study of the complexation of tryptophan, phenylalanine and tyrosine amino acids with cucurbit[7]uril. J INCL PHENOM MACRO 2021. [DOI: 10.1007/s10847-021-01113-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
23
|
Roux A, Talon R, Alsalman Z, Engilberge S, D'Aléo A, Di Pietro S, Robin A, Bartocci A, Pilet G, Dumont E, Wagner T, Shima S, Riobé F, Girard E, Maury O. Influence of Divalent Cations in the Protein Crystallization Process Assisted by Lanthanide-Based Additives. Inorg Chem 2021; 60:15208-15214. [PMID: 34597021 DOI: 10.1021/acs.inorgchem.1c01635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of lanthanide complexes as powerful auxiliaries for biocrystallography prompted us to systematically analyze the influence of the commercial crystallization kit composition on the efficiency of two lanthanide additives: [Eu(DPA)3]3- and Tb-Xo4. This study reveals that the tris(dipicolinate) complex presents a lower chemical stability and a strong tendency toward false positives, which are detrimental for its use in a high-throughput robotized crystallization platform. In particular, the crystal structures of (Mg(H2O)6)3[Eu(DPA)3]2·7H2O (1), {(Ca(H2O)4)3[Eu(DPA)3]2}n·10nH2O (2), and {Cu(DPA)(H2O)2}n (3), resulting from spontaneous crystallization in the presence of a divalent alkaline-earth cation and transmetalation, are reported. On the other hand, Tb-Xo4 is perfectly soluble in the crystallization media, stable in the presence of alkaline-earth dications, and slowly decomposes (within days) by transmetalation with transition metals. The original structure of [Tb4L4(H2O)4]Cl4·15H2O (4) is also described, where L represents a bis(pinacolato)triazacyclononane ligand. This paper also highlights a potential synergy of interactions between Tb-Xo4 and components of the crystallization mixtures, leading to the formation of complex adducts like {AdkA/Tb-Xo4/Mg2+/glycerol} in the protein binding sites. The observation of such multicomponent adducts illustrated the complexity and versatility of the supramolecular chemistry occurring at the surface of the proteins.
Collapse
Affiliation(s)
- Amandine Roux
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France.,Polyvalan, Lyon F-69342, France
| | - Romain Talon
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Zaynab Alsalman
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | | | - Anthony D'Aléo
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Sebastiano Di Pietro
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Adeline Robin
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Alessio Bartocci
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Guillaume Pilet
- CNRS UMR 5615, Université Lyon, Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, Villeurbanne Cedex F-69622, France
| | - Elise Dumont
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France.,Institut Universitaire de France, 1 rue Descartes, Paris 75005, France
| | - Tristan Wagner
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg D-35043, Germany.,Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, 1-Celsiusstrasse, Bremen 35043, Germany
| | - Seigo Shima
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg D-35043, Germany
| | - François Riobé
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Eric Girard
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Olivier Maury
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| |
Collapse
|
24
|
Mendoza J, Cruz L, de Freitas V, Pina F, Basílio N. Anthocyanin Color Stabilization by Host-Guest Complexation with p-Sulfonatocalix[n]arenes. Molecules 2021; 26:molecules26175389. [PMID: 34500822 PMCID: PMC8434021 DOI: 10.3390/molecules26175389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Flavylium-based compounds in their acidic and cationic form bring color to aqueous solutions, while under slightly acidic or neutral conditions they commonly bring discoloration. Selective host-guest complexation between water-soluble p-sulfonatocalix[n]arenes (SCn) macrocycles and the flavylium cationic species can increase the stability of the colored form, expanding its domain over the pH scale. The association constants between SCn and the cationic (acid) and neutral basic forms of flavylium-based compounds were determined through UV-Vis host-guest titrations at different pH values. The affinity of the hosts for synthetic chromophore was found to be higher than for a natural anthocyanin (Oenin). The higher affinity of SC4 for the synthetic flavylium was confirmed by 1H NMR showing a preferential interaction of the flavylium phenyl ring with the host cavity. In contrast with its synthetic counterpart, the flavylium substitution pattern in the anthocyanin seems to limit the inclusion of the guest in the host’s binding pocket. In this case, the higher affinity was observed for the octamer (SC8) likely due to its larger cavity and higher number of negatively charged sulfonate groups.
Collapse
Affiliation(s)
- Johan Mendoza
- LAQV—REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Correspondence: (J.M.); (N.B.)
| | - Luis Cruz
- LAQV—REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal; (L.C.); (V.d.F.)
| | - Victor de Freitas
- LAQV—REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal; (L.C.); (V.d.F.)
| | - Fernando Pina
- LAQV—REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
| | - Nuno Basílio
- LAQV—REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Correspondence: (J.M.); (N.B.)
| |
Collapse
|
25
|
Guillory X, Hadrović I, de Vink PJ, Sowislok A, Brunsveld L, Schrader T, Ottmann C. Supramolecular Enhancement of a Natural 14-3-3 Protein Ligand. J Am Chem Soc 2021; 143:13495-13500. [PMID: 34427424 DOI: 10.1021/jacs.1c07095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational design of protein-protein interaction (PPI) inhibitors is challenging. Connecting a general supramolecular protein binder with a specific peptidic ligand provides a novel conceptual approach. Thus, lysine-specific molecular tweezers were conjugated to a peptide-based 14-3-3 ligand and produced a strong PPI inhibitor with 100-fold elevated protein affinity. X-ray crystal structure elucidation of this supramolecular directed assembly provides unique molecular insight into the binding mode and fully aligns with Molecular Dynamics (MD) simulations. This new supramolecular chemical biology concept opens the path to novel chemical tools for studying PPIs.
Collapse
Affiliation(s)
- Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Inesa Hadrović
- Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Pim J de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Andrea Sowislok
- University Clinics Essen, Experimental Orthopedics and Trauma Surgery, 45147 Essen, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Thomas Schrader
- Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| |
Collapse
|
26
|
Fang Y, He Q, Cao J. Targeted protein degradation and regulation with molecular glue: past and recent discoveries. Curr Med Chem 2021; 29:2490-2503. [PMID: 34365941 DOI: 10.2174/0929867328666210806113949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
The evolution in research and clinical settings of targeted therapies has been inspired by the progress of cancer chemotherapy to use small molecules and monoclonal antibodies for targeting specific disease-associated genes and proteins for noninfectious chronic diseases. In addition to conventional protein inhibition and activation strategies as drug discovery modalities, new methods of targeted protein degradation and regulation using molecular glues have become an attractive approach for drug discovery. Mechanistically, molecular glues trigger interactions between the proteins that originally did not interact by forming ternary complexes as protein-protein interaction (PPI) modulators. New molecular glues and their mechanisms of action have been actively investigated in the past decades. An immunomodulatory imide drug, thalidomide, and its derivatives have been used in the clinic and are a class of molecular glue that induces degradation of several neo-substrates. In this review, we summarize the development of molecular glues and share our opinions on the identification of novel molecular glues in an attempt to promote the concept and inspire further investigations.
Collapse
Affiliation(s)
- Yizheng Fang
- College of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing. China
| | - Qiaojun He
- Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou. China
| | - Ji Cao
- The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou. China
| |
Collapse
|
27
|
Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages. Chemistry 2021; 27:9542-9549. [PMID: 33904620 PMCID: PMC8362067 DOI: 10.1002/chem.202100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 12/15/2022]
Abstract
The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.
Collapse
Affiliation(s)
- Lucía Tapia
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Naiara Solozabal
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Yolanda Pérez
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - W. Todd Miller
- Department of Physiology and BiophysicsStony Brook University and Department of Veterans Affairs Medical CenterStony BrookNY, 11794USA
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| |
Collapse
|
28
|
Mockler NM, Engilberge S, Rennie ML, Raston CL, Crowley PB. Protein-macrocycle framework engineering: supramolecular copolymerisation with two disparate calixarenes. Supramol Chem 2021. [DOI: 10.1080/10610278.2021.1935946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Niamh M. Mockler
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Colin L Raston
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Bedford Park SA Adelaide, Australia
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| |
Collapse
|
29
|
Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Wenbing Cao
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhen Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xianyin Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Weimin Xuan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yingming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| |
Collapse
|
30
|
Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021; 60:11196-11200. [PMID: 33580548 DOI: 10.1002/anie.202100916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Indexed: 01/24/2023]
Abstract
Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Using two enzymes and a cytokine as models, we showed that the activity of proteins bearing unnatural amino acid could be turned off by host molecule binding, which blocked its functional binding surface. Protein activity can be switched back by treatment with a competitive guest molecule. Our approach provides a general tool for reversibly regulating protein function through molecular recognition and can be expected to be valuable for studying protein functions.
Collapse
Affiliation(s)
- Wenbing Cao
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhen Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xianyin Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Weimin Xuan
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yingming Zhang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| |
Collapse
|
31
|
Gao W, Wang Y, Zhang F, Zhang S, Lian HZ. Tetrasulfonate calix[4]arene modified large pore mesoporous silica microspheres: Synthesis, characterization, and application in protein separation. Talanta 2021; 226:122171. [PMID: 33676713 DOI: 10.1016/j.talanta.2021.122171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 10/22/2022]
Abstract
Effective protein adsorption by solid matrices from complex biological samples has attracted attention for broad application in biomedical field. Immobilization of calixarenes to solid supports is an essential process for their application in protein separation and purification. Silica is the most widely used support material in calixarene immobilization. With high concentration of polymer microspheres as templates, the large pore mesoporous silica microspheres with controllable, uniform size and structure were successfully synthesized and the resulting large pore mesoporous silica microspheres were modified with water-soluble tetrasulfonate calix[4]arene of unique hollow cavity-shaped structure. The tetrasulfonate calix[4]arene modified large pore mesoporous silica microspheres (SCLX4@LPMS) were characterized by diverse analytical techniques and their protein adsorption performance were also investigated. The obtained SCLX4@LPMS gave rise to an adsorption efficiency of >90% for cytochrome c and lysozyme within a wide pH range of 3.0-10.0 and possessed remarkably high adsorption capacity of cytochrome c (363.64 mg g-1) and lysozyme (166.11 mg g-1). The retained cytochrome c and lysozyme can be readily eluted by using phosphate buffer solution containing NaCl as a stripping reagent with the recoveries of 81% and 86% after 5 times enrichment, respectively. The SCLX4@LPMS microspheres have been applied for the selective adsorption of proteins in real samples and had the application potential in protein adsorption, drug delivery, biosensors, and other biomedical fields.
Collapse
Affiliation(s)
- Wei Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Ye Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Feng Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Sen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Hong-Zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China.
| |
Collapse
|
32
|
de Vink PJ, van der Hek T, Brunsveld L. Light-driven release of cucurbit[8]uril from a bivalent cage. Chem Sci 2021; 12:6726-6731. [PMID: 34040748 PMCID: PMC8132991 DOI: 10.1039/d1sc01410b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/10/2021] [Indexed: 12/03/2022] Open
Abstract
Temporal control over supramolecular systems has great potential for the modulation of binding and assembly events, such as providing orthogonal control over protein activity. Especially light controlled triggering provides unique entries for supramolecular systems to interface in a controlled manner with enzymes. Here we report on the light-induced release of cucurbit[8]uril (CB[8]) from a bivalent cage molecule and its subsequent activation of a proteolytic enzyme, caspase-9, that itself is unresponsive to light. Central to the design is the bivalent binding of the cage with high affinity to CB[8], 100-fold stronger than the UV-inactivated products. The affinity switching occurs in the (sub-)micromolar concentration regime, matching the concentration characteristics required for dimerizing and activating caspase-9 by CB[8]. The light-responsive caged CB[8] concept presented offers a novel platform for tuning and application of switchable cucurbiturils and beyond.
Collapse
Affiliation(s)
- Pim J de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Tim van der Hek
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| |
Collapse
|
33
|
Meiners A, Bäcker S, Hadrović I, Heid C, Beuck C, Ruiz-Blanco YB, Mieres-Perez J, Pörschke M, Grad JN, Vallet C, Hoffmann D, Bayer P, Sánchez-García E, Schrader T, Knauer SK. Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
Collapse
Affiliation(s)
- Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sandra Bäcker
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Inesa Hadrović
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Heid
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Marius Pörschke
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Cecilia Vallet
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sánchez-García
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Shirley K Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| |
Collapse
|
34
|
Mockler N, Ramberg KO, Guagnini F, Raston CL, Crowley PB. Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with α-Helical Recognition Properties. CRYSTAL GROWTH & DESIGN 2021; 21:1424-1427. [PMID: 34054353 PMCID: PMC8154262 DOI: 10.1021/acs.cgd.0c01717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Water-soluble, anionic calix[n]arenes are useful receptors for protein recognition and assembly. For example, sulfonato-calix[8]arene (sclx 8 ) can encapsulate proteins and direct their assembly into porous frameworks. In this work, we turned our attention to an "extended arm" calixarene with 16 phenyl rings. We hypothesized that this larger receptor would have increased capacity for protein masking/encapsulation. A cocrystal structure of p-benzyl-sulfonato-calix[8]arene (b-sclx 8 ) and cytochrome c (cyt c) revealed a surprising assembly. A pseudorotaxane comprising a stack of three b-sclx 8 molecules threaded by polyethylene glycol (PEG) was bound to the protein. The trimeric b-sclx 8 stack, a tubelike structure with a highly charged surface, mediated assembly via a new mode of protein recognition. The calixarene stack presents four hydrophobic grooves, each of which binds to one cyt c by accommodating the N-terminal α-helix. This unprecedented binding mode suggests new possibilities for supramolecular protein chemistry.
Collapse
Affiliation(s)
- Niamh
M. Mockler
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Kiefer O. Ramberg
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Francesca Guagnini
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Colin L. Raston
- Flinders
Institute for Nanoscale Science and Technology, College of Science
and Engineering, Flinders University, Bedford Park, South 5042, Australia
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| |
Collapse
|
35
|
Dutta Choudhury S, Pal H. Supramolecular and suprabiomolecular photochemistry: a perspective overview. Phys Chem Chem Phys 2021; 22:23433-23463. [PMID: 33112299 DOI: 10.1039/d0cp03981k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this perspective review article, we have attempted to bring out the important current trends of research in the areas of supramolecular and suprabiomolecular photochemistry. Since the spans of the subject areas are very vast, it is impossible to cover all the aspects within the limited space of this review article. Nevertheless, efforts have been made to assimilate the basic understanding of how supramolecular interactions can significantly change the photophysical and other related physiochemical properties of chromophoric dyes and drugs, which have enormous academic and practical implications. We have discussed with reference to relevant chemical systems where supramolecularly assisted modulations in the properties of chromophoric dyes and drugs can be used or have already been used in different areas like sensing, dye/drug stabilization, drug delivery, functional materials, and aqueous dye laser systems. In supramolecular assemblies, along with their conventional photophysical properties, the acid-base properties of prototropic dyes, as well as the excited state prototautomerization and related proton transfer behavior of proton donor/acceptor dye molecules, are also largely modulated due to supramolecular interactions, which are often reflected very explicitly through changes in their absorption and fluorescence characteristics, providing us many useful insights into these chemical systems and bringing out intriguing applications of such changes in different applied areas. Another interesting research area in supramolecular photochemistry is the excitation energy transfer from the donor to acceptor moieties in self-assembled systems which have immense importance in light harvesting applications, mimicking natural photosynthetic systems. In this review article, we have discussed varieties of these aspects, highlighting their academic and applied implications. We have tried to emphasize the progress made so far and thus to bring out future research perspectives in the subject areas concerned, which are anticipated to find many useful applications in areas like sensors, catalysis, electronic devices, pharmaceuticals, drug formulations, nanomedicine, light harvesting, and smart materials.
Collapse
Affiliation(s)
- Sharmistha Dutta Choudhury
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India. and Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai-400094, India
| | - Haridas Pal
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai-400094, India and Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India.
| |
Collapse
|
36
|
Zhou J, Rao L, Yu G, Cook TR, Chen X, Huang F. Supramolecular cancer nanotheranostics. Chem Soc Rev 2021; 50:2839-2891. [PMID: 33524093 DOI: 10.1039/d0cs00011f] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Among the many challenges in medicine, the treatment and cure of cancer remains an outstanding goal given the complexity and diversity of the disease. Nanotheranostics, the integration of therapy and diagnosis in nanoformulations, is the next generation of personalized medicine to meet the challenges in precise cancer diagnosis, rational management and effective therapy, aiming to significantly increase the survival rate and improve the life quality of cancer patients. Different from most conventional platforms with unsatisfactory theranostic capabilities, supramolecular cancer nanotheranostics have unparalleled advantages in early-stage diagnosis and personal therapy, showing promising potential in clinical translations and applications. In this review, we summarize the progress of supramolecular cancer nanotheranostics and provide guidance for designing new targeted supramolecular theranostic agents. Based on extensive state-of-the-art research, our review will provide the existing and new researchers a foundation from which to advance supramolecular cancer nanotheranostics and promote translationally clinical applications.
Collapse
Affiliation(s)
- Jiong Zhou
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China.
| | | | | | | | | | | |
Collapse
|
37
|
Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors. Molecules 2020; 26:molecules26010106. [PMID: 33379401 PMCID: PMC7796322 DOI: 10.3390/molecules26010106] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.
Collapse
|
38
|
Bartocci A, Gillet N, Jiang T, Szczepaniak F, Dumont E. Molecular Dynamics Approach for Capturing Calixarene-Protein Interactions: The Case of Cytochrome C. J Phys Chem B 2020; 124:11371-11378. [PMID: 33270456 DOI: 10.1021/acs.jpcb.0c08482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant proteins and ligands. We characterize two main binding sites for the sulfonated calixarene on the cytochrome c surface which are in perfect agreement with the previous experiments with regard to the structure (comparison with the X-ray structure PDB 6GD8) and the binding free energies [comparison between the molecular mechanics Poisson-Boltzmann surface area analysis and the isothermal titration calorimetry measurements]. The per-residue decomposition of the interaction energies reveals the detailed picture of this electrostatically driven association and notably the role of arginine R13 as a bridging residue between the two main anchoring sites. In addition, the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of a hydrogen bond network far from the binding sites, increasing the rigidity of the protein. This study paves the way toward an automated procedure to predict the supramolecular protein-cage association, with the possibility of a computational screening of new promising derivatives for controlled protein assembly and protein surface recognition processes.
Collapse
Affiliation(s)
- Alessio Bartocci
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Natacha Gillet
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Tao Jiang
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Florence Szczepaniak
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Elise Dumont
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.,Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
| |
Collapse
|
39
|
Synthesis and Glycosidase Inhibition Properties of Calix[8]arene-Based Iminosugar Click Clusters. Pharmaceuticals (Basel) 2020; 13:ph13110366. [PMID: 33167387 PMCID: PMC7694328 DOI: 10.3390/ph13110366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
A set of 6- to 24-valent clusters was constructed with terminal deoxynojirimycin (DNJ) inhibitory heads through C6 or C9 linkers by way of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions between mono- or trivalent azido-armed iminosugars and calix[8]arene scaffolds differing in their valency and their rigidity but not in their size. The power of multivalency to upgrade the inhibition potency of the weak DNJ inhibitor (monovalent DNJ Ki being at 322 and 188 µM for C6 or C9 linkers, respectively) was evaluated on the model glycosidase Jack Bean α-mannosidase (JBα-man). Although for the clusters with the shorter C6 linker the rigidity of the scaffold was essential, these parameters had no influence for clusters with C9 chains: all of them showed rather good relative affinity enhancements per inhibitory epitopes between 70 and 160 highlighting the sound combination of the calix[8]arene core and the long alkyl arms. Preliminary docking studies were performed to get insights into the preferred binding modes.
Collapse
|
40
|
Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
Collapse
Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| |
Collapse
|
41
|
Di Costanzo L, Geremia S. Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins. Molecules 2020; 25:E3555. [PMID: 32759758 PMCID: PMC7435792 DOI: 10.3390/molecules25153555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.
Collapse
Affiliation(s)
- Luigi Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, 100, 80055 Portici, Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
| |
Collapse
|
42
|
Cationic Pillar[6]arene Induces Cell Apoptosis by Inhibiting Protein Tyrosine Phosphorylation Via Host-Guest Recognition. Int J Mol Sci 2020; 21:ijms21144979. [PMID: 32679647 PMCID: PMC7404071 DOI: 10.3390/ijms21144979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
We reported for the first time that cationic pillar[6]arene (cPA6) could tightly bind to peptide polymer (MW~20–50 kDa), an artificial substrate for tyrosine (Tyr) phosphorylation, and efficiently inhibit Tyr protein phosphorylation through host–guest recognition. We synthesized a nanocomposite of black phosphorus nanosheets loaded with cPA6 (BPNS@cPA6) to explore the effect of cPA6 on cells. BPNS@cPA6 was able to enter HepG2 cells, induced apoptosis, and inhibited cell proliferation by reducing the level of Tyr phosphorylation. Furthermore, BPNS@cPA6 showed a stronger ability of inhibiting cell proliferation in tumor cells than in normal cells. Our results revealed the supramolecular modulation of enzymatic Tyr phosphorylation by the host–guest recognition of cPA6.
Collapse
|
43
|
Goh CY, Fu DY, Duncan CL, Tinker A, Li F, Mocerino M, Ogden MI, Wu Y. The inhibitory properties of acidic functionalised calix[4]arenes on human papillomavirus pentamer formation. Supramol Chem 2020. [DOI: 10.1080/10610278.2020.1779930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ching Yong Goh
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Ding-Yi Fu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun, China
- School of Pharmacy, Nantong University, Nantong, China
| | - Caitlin L. Duncan
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Adam Tinker
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Mauro Mocerino
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Mark I. Ogden
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| |
Collapse
|
44
|
Zhao H, Yang XH, Pan YC, Tian HW, Hu XY, Guo DS. Inhibition of insulin fibrillation by amphiphilic sulfonatocalixarene. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.01.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
45
|
Bonding of crown ethers to α-zirconium phosphate—Novel layered adsorbent for radioactive strontium separation. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.116658] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
46
|
Baldini L, Casnati A, Sansone F. Multivalent and Multifunctional Calixarenes in Bionanotechnology. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000255] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Laura Baldini
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Alessandro Casnati
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Francesco Sansone
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| |
Collapse
|
47
|
Dai L, Feng WX, Zheng SP, Jiang JJ, Wang D, van der Lee A, Dumitrescu D, Barboiu M. Progressive Folding and Adaptive Multivalent Recognition of Alkyl Amines and Amino Acids in p-Sulfonatocalix[4]arene Hosts: Solid-State and Solution Studies. Chempluschem 2020; 85:1623-1631. [PMID: 32286737 DOI: 10.1002/cplu.202000232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Indexed: 01/15/2023]
Abstract
Calix[4]arenes have the ability to encapsulate biomimetic guests, offering interesting opportunities to explore their molecular recognition, very close to biological scenarios. In this study, p-sulfonatocalix[4]arene (C4 A) anions and hydrated alkali cations have been used for the in situ recognition of cationic 1,ω-diammonium-alkanes and 1,ω-amino-acids of variable lengths. NMR spectroscopy illustrates that these systems are stable in aqueous solution and the interaction process involves several binding states or stabilized conformations within the C4 A anion, depending of the nature of the guest. DOSY experiments showed that monomeric 1 : 1 host-guest species are present, while the cation does not influence their self-assembly in solution. The folded conformations observed in the solid-state X-ray single-crystal structures shed light on the constitutional adaptivity of flexible chains to environmental factors. Futhermore, a comprehensive screening of 30 single crystal structures helped to understand the in situ conformational fixation and accurate determination of the folded structures of the confined guest molecules, with a compression up to 40 % compared with their linear conformations.
Collapse
Affiliation(s)
- Liya Dai
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Wei-Xu Feng
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shannxi, 710129, P. R. China
| | - Shao-Ping Zheng
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Ji-Jun Jiang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Dawei Wang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Arie van der Lee
- Institut Europeen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM-CNRS, Place E. Bataillon CC047, 34095, Montpellier, France
| | - Dan Dumitrescu
- XRD2 beamline, Elettra - Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Mihail Barboiu
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.,Institut Europeen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM-CNRS, Place E. Bataillon CC047, 34095, Montpellier, France
| |
Collapse
|
48
|
Humbert N, Kovalenko L, Saladini F, Giannini A, Pires M, Botzanowski T, Cherenok S, Boudier C, Sharma KK, Real E, Zaporozhets OA, Cianférani S, Seguin-Devaux C, Poggialini F, Botta M, Zazzi M, Kalchenko VI, Mori M, Mély Y. (Thia)calixarenephosphonic Acids as Potent Inhibitors of the Nucleic Acid Chaperone Activity of the HIV-1 Nucleocapsid Protein with a New Binding Mode and Multitarget Antiviral Activity. ACS Infect Dis 2020; 6:687-702. [PMID: 32045204 DOI: 10.1021/acsinfecdis.9b00290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nucleocapsid protein (NC) is a highly conserved protein that plays key roles in HIV-1 replication through its nucleic acid chaperone properties mediated by its two zinc fingers and basic residues. NC is a promising target for antiviral therapy, particularly to control viral strains resistant to currently available drugs. Since calixarenes with antiviral properties have been described, we explored the ability of calixarene hydroxymethylphosphonic or sulfonic acids to inhibit NC chaperone properties and exhibit antiviral activity. By using fluorescence-based assays, we selected four calixarenes inhibiting NC chaperone activity with submicromolar IC50 values. These compounds were further shown by mass spectrometry, isothermal titration calorimetry, and fluorescence anisotropy to bind NC with no zinc ejection and to compete with nucleic acids for the binding to NC. Molecular dynamic simulations further indicated that these compounds interact via their phosphonate or sulfonate groups with the basic surface of NC but not with the hydrophobic plateau at the top of the folded fingers. Cellular studies showed that the most soluble compound CIP201 inhibited the infectivity of wild-type and drug-resistant HIV-1 strains at low micromolar concentrations, primarily targeting the early steps of HIV-1 replication. Moreover, CIP201 was also found to inhibit the flipping and polymerization activity of reverse transcriptase. Calixarenes thus form a class of noncovalent NC inhibitors, endowed with a new binding mode and multitarget antiviral activity.
Collapse
Affiliation(s)
- Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
- Department of Chemistry, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Manuel Pires
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Sergiy Cherenok
- Institute of Organic Chemistry, National Academy of Science of Ukraine, Murmanska str. 5, Kyiv 02660, Ukraine
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Kamal K. Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Olga A. Zaporozhets
- Department of Chemistry, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Federica Poggialini
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Vitaly I. Kalchenko
- Institute of Organic Chemistry, National Academy of Science of Ukraine, Murmanska str. 5, Kyiv 02660, Ukraine
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| |
Collapse
|
49
|
Alex JM, Brancatelli G, Volpi S, Bonaccorso C, Casnati A, Geremia S, Crowley PB. Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene. Org Biomol Chem 2020; 18:211-214. [DOI: 10.1039/c9ob02275a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In contrast to sulfonato-calix[4]arene (sclx4), which mediates close-packed assemblies, the higher charge carboxylate-containing sclx4mc induced a crystalline framework of cytochrome c.
Collapse
Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
| | - Giovanna Brancatelli
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Carmela Bonaccorso
- Dipartimento di Scienze Chimiche
- Università degli Studi di Catania
- Catania
- Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
| |
Collapse
|
50
|
Engilberge S, Rennie ML, Dumont E, Crowley PB. Tuning Protein Frameworks via Auxiliary Supramolecular Interactions. ACS NANO 2019; 13:10343-10350. [PMID: 31490058 DOI: 10.1021/acsnano.9b04115] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein crystals with their precise, periodic array of functional building blocks have potential applications in biomaterials, sensing, and catalysis. This paper describes how a highly porous crystalline framework of a cationic redox protein and an anionic macrocycle can be modulated by a small cationic effector. Ternary composites of protein (∼13 kDa), calix[8]arene (∼1.5 kDa), and effector (∼0.2 kDa) formed distinct crystalline architectures, dependent on the effector concentration and the crystallization technique. A combination of X-ray crystallography and density functional theory (DFT) calculations was used to decipher the framework variations, which appear to be dependent on a calixarene conformation change mediated by the effector. This "switch" calixarene was observed in three states, each of which is associated with a different interaction network. Two structures obtained by co-crystallization with the effector contained an additional protein "pillar", resulting in framework duplication and decreased porosity. These results suggest how protein assembly can be engineered by supramolecular host-guest interactions.
Collapse
Affiliation(s)
- Sylvain Engilberge
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Martin L Rennie
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , 69342 Lyon , France
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| |
Collapse
|